I suspect the drives must both be NTFS or the Junction command would have failed.
The current backup may be in an inconsistent state. You may need to go to Edit > Preferences > Devices and delete the backup for the device before attempting to backup again.
You can check that the redirection is in force by typing junction -s c:\ at the command prompt (in the folder where Junction is). Alternatively you can create a dummy text file in the F:\Backup folder and see that it shows up when views from the path on the C: drive.